Opportunities and challenges in design and optimization of protein function

D. Listov; C. A. Goverde; B. E. Correia; S. J. Fleishman 

A Synthetic Multivalent Lipopeptide Derived from Pam3CSK4 with Irreversible Influenza Inhibition and Immuno-Stimulating Effects

Y. Zhu; L. Wei; A. C-A. Zwygart; P. Gainza; Q. O. Khac et al. 

An atlas of protein homo-oligomerization across domains of life

H. Schweke; M. Pacesa; T. Levin; C. A. Goverde; P. Kumar et al. 

Predicting protein interactions using geometric deep learning on protein surfaces

A PD-L1/EGFR bispecific antibody combines immune checkpoint blockade and direct anti-cancer action for an enhanced anti-tumor response

L. Rubio-Perez; R. Lazaro-Gorines; S. L. Harwood; M. Compte; R. Navarro et al. 

A new age in protein design empowered by deep learning

H. Khakzad; I. Igashov; A. Schneuing; C. Goverde; M. Bronstein et al. 

Protein-based bandpass filters for controlling cellular signaling with chemical inputs

S. Shui; L. Scheller; B. E. Correia 

Deformation response of highly stretchable and ductile graphene kirigami under uniaxial and biaxial tension

P. Shi; Y. Chen; Y. Wei; J. Feng; T. Guo et al. 

Rational design of small-molecule responsive protein switches

S. Shui; S. Buckley; L. Scheller; B. E. Correia 

Rules and mechanisms governing G protein coupling selectivity of GPCRs

I. Masuho; R. Kise; P. Gainza; E. Von Moo; X. Li et al. 

Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

H. Schweke; Q. Xu; G. Tauriello; L. Pantolini; T. Schwede et al. 

Rational Design of Chemically Controlled Antibodies and Protein Therapeutics

A. Marchand; L. Bonati; S. Shui; L. Scheller; P. Gainza Cirauqui et al. 

De novo protein design by inversion of the AlphaFold structure prediction network

C. Goverde; B. Wolf; H. Khakzad; S. Rosset; B. Correia 

New protein–protein interactions designed by a computer

A. Marchand; P. Gainza Cirauqui 

De novo design of protein interactions with learned surface fingerprints

P. Gainza Cirauqui; S. Wehrle; A. K. Van Hall-Beauvais; A. Marchand; A. Scheck et al. 

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

C. Gueto-Tettay; D. Tang; L. Happonen; M. Heusel; H. Khakzad et al. 

Track: Machine Learning in Protein Science De Novo Design of Viral Epitope Mimetics with Non-Regular Structural Features

K. Castro; J. Wang; L. Milles; J. Watson; R. Ragotte et al. 

De novo designed proteins: a study in engineering novel folds and functions

Computational design of vaccine immunogens

K. M. Castro; A. Scheck; S. Xiao; B. E. Correia 

Invasive Streptococcal Infection Can Lead to the Generation of Cross-Strain Opsonic Antibodies

T. de Neergaard; A. Blaeckberg; H. Ivarsson; S. Thomasson; V. K. Ahnlide et al. 

A generic framework for hierarchical de novo protein design

Z. Harteveld; J. Bonet; S. Rosset; C. Yang; F. Sesterhenn et al. 

Assessing and enhancing foldability in designed proteins

D. Listov; R. Lipsh-Sokolik; S. Rosset; C. Yang; B. E. Correia et al. 

Programmable DARPin-based receptors for the detection of thrombotic markers

T. Strittmatter; Y. Wang; A. Bertschi; L. Scheller; P. C. Freitag et al. 

Antibodies to combat viral infections: development strategies and progress

G. Pantaleo; B. Correia; C. Fenwick; V. S. Joo; L. Perez 

Computational design of novel protein–protein interactions – An overview on methodological approaches and applications

A. Marchand; A. K. Van Hall-Beauvais; B. Correia 

Novel chemically controlled cellular switches

B. E. Correia; S. Shui; P. Gainza Cirauqui 

A method and system for fast end-to-end learning on protein surfaces

M. Bronstein; F. Sverrisson; J. Pierre Feydy; P. Gainza; B. Ferreira De Sousa Correia 

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors

Rational design of protein switches: applications in synthetic biology and cancer immunotherapy

De Novo Design of Site-specific Protein Binders Using Surface Fingerprints

S. Wehrle; A. Van Hall-Beauvais; P. Gainza; Z. Harteveld; A. Scheck et al. 

Computational design of bioactive protein switches with multi-logics for cell-based therapeutics

S. Shui; P. Gainza; L. Scheller; C. Yang; B. Correia 

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

B. Anton; M. Besalu; O. Fornes; J. Bonet; A. Molina et al. 

A Nanoscaffolded Spike-RBD Vaccine Provides Protection against SARS-CoV-2 with Minimal Anti-Scaffold Response

D. Lainšček; T. Fink; V. Forstnerič; I. Hafner-Bratkovič; S. Orehek et al. 

Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning

D. M. Mason; S. Friedensohn; C. R. Weber; C. Jordi; B. Wagner et al. 

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

C. T. Schoeder; S. Schmitz; J. Adolf-Bryfogle; A. M. Sevy; J. A. Finn et al. 

Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein

M. D. Hoffmann; J. Mathony; J. U. Zu Belzen; Z. Harteveld; S. Aschenbrenner et al. 

A Rosetta-based protein design protocol converging to natural sequences

G. Sormani; Z. Harteveld; S. Rosset; B. Correia; A. Laio 

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

J. Aguirre-Plans; A. Meseguer; R. Molina-Fernandez; M. A. Marin-Lopez; G. Jumde et al. 

Bottom-up de novo design of functional proteins with complex structural features

C. Yang; F. Sesterhenn; J. Bonet; E. A. van Aalen; L. Scheller et al. 

Fast end-to-end learning on protein surfaces

F. Sverrisson; J. Feydy; B. E. Correia; M. M. Bronstein 

On the exploration of novel methodological approaches for immunogen design: case studies in influenza and hepatitis C

Preclinical development of a humanized chimeric antigen receptor against B-cell maturation antigen for multiple myeloma

L. Perez-Amill; G. Sune; A. Antonana-Vildosola; M. Castella; A. Najjar et al. 

Oligomerization Profile of Human Transthyretin Variants with Distinct Amyloidogenicity

A. Frangolho; B. Correia; D. C. Vaz; Z. L. Almeida; R. M. M. Brito 

Designs and Characterization of Subunit Ebola GP Vaccine Candidates: Implications for Immunogenicity

V. Agnolon; D. Kiseljak; M. J. Wurm; F. M. Wurm; C. Foissard et al. 

Picometer Resolution Structure of the Coordination Sphere in the Metal-Binding Site in a Metalloprotein by NMR

A. Bertarello; L. Benda; K. J. Sanders; A. J. Pell; M. J. Knight et al. 

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

A. Meseguer; F. Arman; O. Fornes; R. Molina-Fernandez; J. Bonet et al. 

Macromolecular modeling and design in Rosetta: recent methods and frameworks

J. K. Leman; B. D. Weitzner; S. M. Lewis; J. Adolf-Bryfogle; N. Alam et al. 

De novo protein design enables the precise induction of RSV-neutralizing antibodies

F. Sesterhenn; C. Yang; J. Bonet; J. T. Cramer; X. Wen et al. 

Computational design of anti-CRISPR proteins with improved inhibition potency

J. Mathony; Z. Harteveld; C. Schmelas; J. U. zu Belzen; S. Aschenbrenner et al. 

Structural basis for recognition of RALF peptides by LRX proteins during pollen tube growth

S. Moussu; C. Broyart; G. Santos-Fernandez; S. Augustin; S. Wehrle et al. 

Epitope Mapping and Fine Specificity of Human T and B Cell Responses for Novel Candidate Blood-Stage Malaria Vaccine P27A

K. M. Geiger; D. Guignard; C. Yang; J-P. Bikorimana; B. E. Correia et al. 

A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy

G. Giordano-Attianese; P. Gainza; E. Gray-Gaillard; E. Cribioli; S. Shui et al. 

The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase

M. J. C. Long; A. Van Hall-Beauvais; Y. Aye 

Immunogen

B. Correia; F. Sesterhenn; C. Yang; J. Bonet 

Immunogen

B. Correia; F. Sesterhenn 

Functional de novo Protein Design for Targeted Vaccines and Synthetic Biology Applications

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

P. Gainza; F. Sverrisson; F. Monti; E. Rodolà; D. Boscaini et al. 

Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-alpha 7 mediated nuclear import pathway

P. Resa-Infante; J. Bonet; S. Thiele; M. Alawi; S. Stanelle-Bertram et al. 

Decrypting interaction fingerprints in protein molecular surfaces

P. Gainza; F. Sverrisson; F. Monti; M. Bronstein; B. Correia 

rstoolbox – a Python library for large-scale analysis of computational protein design data and structural bioinformatics

J. Bonet; Z. Harteveld; F. Sesterhenn; A. Scheck; B. E. Correia 

Engineered Anti-CRISPR Proteins for Precision Control of CRISPR-Cas9

F. Bubeck; M. D. Hoffmann; Z. Harteveld; S. Aschenbrenner; A. Bietz et al. 

Heterodimeric inactivatable chimeric antigen receptors

G. Coukos; M. Irving; B. Correia; P. Gainza-Cirauqui; G. Giordano Attianese 

Expanding beyond the natural protein repertoire to engineer targeted vaccines and diagnostics

Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen

J. Munro; F. Sesterhenn; M. Galloux; S. S. Vollers; L. Csepregi et al. 

Rosetta FunFolDes – A general framework for the computational design of functional proteins

J. Bonet; S. Wehrle; K. Schriever; C. Yang; A. Billet et al. 

Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9

F. Bubeck; M. D. Hoffmann; Z. Harteveld; S. Aschenbrenner; A. Bietz et al. 

Driving Immune Responses with Synthetic Proteins – Development of De Novo Designed Immunogens to Elicit Respiratory Syncytial Virus Neutralizing Antibodies

F. Sesterhenn; C. Yang; J. Bonet; M. Galloux; X. Wen et al. 

Design and characterization of near-native Ebola GP vaccine candidates: implications for immunogenicity

V. Agnolon; I. Ayadi; J. P. Bikorimana; D. Kiseljak; V. De Vaux et al. 

Expanding the druggable proteome: Ligand and target discovery by fragment-based screening in cells

C. Parker; A. Galmozzi; Y. Wang; B. Correia; E. Saez et al. 

Structure-based immunogen design – leading the way to the new age of precision vaccines

F. Sesterhenn; J. Bonet; B. E. Correia 

OFF-switch CAR T cell for safety-enhanced cancer immunotherapy

E. F. Gray-Gaillard; G. G. Attianese; P. Gainza-Cirauqui; S. Vollers; S. Shui et al. 

On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures

M. Marin-Lopez; J. Planas-Iglesias; J. Aguirre-Plans; J. Bonet; J. Garcia-Garcia et al. 

Computational protein design – the next generation tool to expand synthetic biology applications

P. Gainza-Cirauqui; B. Correia 

Bispecific light T-cell engagers for gene-based immunotherapy of epidermal growth factor receptor (EGFR)-positive malignancies

K. Molgaard; S. Harwood; M. Compte; N. Merino; J. Bonet et al. 

ATTACK, a novel bispecific T cell-recruiting antibody with trivalent EGFR binding and monovalent CD3 binding for cancer immunotherapy

S. Harwood; A. Alvarez-Cienfuegos; N. Nunez-Prado; M. Compte; S. Hernandez-Perez et al. 

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

E. Sarti; I. Gladich; S. Zamuner; B. E. Correia; A. Laio 

InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research

D. Poglayen; M. Alejandro Marin-Lopez; J. Bonet; O. Fornes; J. Garcia-Garcia et al. 

Understanding protein recognition using structural features

M. A. Marin-Lopez; J. Planas-Iglesias; J. Bonet; D. Poglayen; J. Garcia-Garcia et al. 

Proof of principle for epitope-focused vaccine design

B. Correia; J. Bates; R. Loomis; C. Carrico; J. Jardine et al.